Table 2.
Significantly enriched GO terms (Biological Process Ontology) in the subsets of differentially expressed genes (p-value < 0.05)
| GO.ID | Term | Annotated | Significant | Expected | p-value |
|---|---|---|---|---|---|
| Overrepresented in the subset of up-regulated in local infection | |||||
| GO:0006351 | transcription, DNA-templated | 2046 | 271 | 151.48 | 1.8E-22 |
| GO:0006310 | DNA recombination | 47 | 15 | 3.48 | 2.5E-06 |
| GO:0005992 | trehalose biosynthetic process | 34 | 12 | 2.52 | 3.1E-06 |
| GO:0048544 | recognition of pollen | 69 | 16 | 5.11 | 0.000034 |
| GO:0006302 | double-strand break repair | 16 | 7 | 1.18 | 0.000076 |
| GO:0006464 | cellular protein modification process | 2490 | 237 | 184.35 | 0.00008 |
| GO:0006012 | galactose metabolic process | 23 | 8 | 1.7 | 0.00016 |
| GO:0006950 | response to stress | 873 | 108 | 64.63 | 0.00022 |
| GO:0016310 | phosphorylation | 2148 | 196 | 159.03 | 0.00023 |
| GO:0006376 | mRNA splice site selection | 6 | 4 | 0.44 | 0.0004 |
| GO:0032968 | positive regulation of transcription elongation from RNA polymerase II promoter | 3 | 3 | 0.22 | 0.00041 |
| GO:0006887 | exocytosis | 72 | 14 | 5.33 | 0.00071 |
| GO:0006635 | fatty acid beta-oxidation | 7 | 4 | 0.52 | 0.00087 |
| GO:0006281 | DNA repair | 271 | 38 | 20.06 | 0.00415 |
| GO:0043562 | cellular response to nitrogen levels | 2 | 2 | 0.15 | 0.00548 |
| GO:0009744 | response to sucrose | 2 | 2 | 0.15 | 0.00548 |
| GO:0045454 | cell redox homeostasis | 229 | 28 | 16.95 | 0.00608 |
| GO:0008272 | sulfate transport | 31 | 7 | 2.3 | 0.00653 |
| GO:0000160 | phosphorelay signal transduction system | 102 | 15 | 7.55 | 0.00799 |
| GO:0006334 | nucleosome assembly | 59 | 10 | 4.37 | 0.01074 |
| GO:0009298 | GDP-mannose biosynthetic process | 7 | 3 | 0.52 | 0.0113 |
| GO:0070966 | nuclear-transcribed mRNA catabolic process, no-go decay | 3 | 2 | 0.22 | 0.01562 |
| GO:0070481 | nuclear-transcribed mRNA catabolic process, non-stop decay | 3 | 2 | 0.22 | 0.01562 |
| GO:0071025 | RNA surveillance | 3 | 2 | 0.22 | 0.01562 |
| GO:0015706 | nitrate transport | 3 | 2 | 0.22 | 0.01562 |
| GO:0010167 | response to nitrate | 3 | 2 | 0.22 | 0.01562 |
| GO:0007064 | mitotic sister chromatid cohesion | 8 | 3 | 0.59 | 0.01709 |
| GO:0006032 | chitin catabolic process | 31 | 6 | 2.3 | 0.02419 |
| GO:0035434 | copper ion transmembrane transport | 9 | 3 | 0.67 | 0.02425 |
| GO:0050832 | defense response to fungus | 4 | 2 | 0.3 | 0.02972 |
| GO:0042742 | defense response to bacterium | 4 | 2 | 0.3 | 0.02972 |
| GO:0007050 | cell cycle arrest | 10 | 3 | 0.74 | 0.03277 |
| GO:0006529 | asparagine biosynthetic process | 11 | 3 | 0.81 | 0.04263 |
| GO:0006020 | inositol metabolic process | 11 | 3 | 0.81 | 0.04263 |
| Overrepresented in the subset of down-regulated in local infection | |||||
| GO:0009765 | photosynthesis, light harvesting | 74 | 61 | 12.92 | 1E-30 |
| GO:0007017 | microtubule-based process | 254 | 105 | 44.35 | 4.6E-19 |
| GO:0033014 | tetrapyrrole biosynthetic process | 53 | 32 | 9.25 | 3.3E-12 |
| GO:0015979 | photosynthesis | 387 | 169 | 67.57 | 4.9E-12 |
| GO:0000079 | regulation of cyclin-dependent protein serine/threonine kinase activity | 48 | 29 | 8.38 | 3.4E-11 |
| GO:0006270 | DNA replication initiation | 18 | 16 | 3.14 | 7.7E-11 |
| GO:0072330 | monocarboxylic acid biosynthetic process | 171 | 61 | 29.85 | 8.1E-09 |
| GO:0051258 | protein polymerization | 86 | 34 | 15.01 | 8.8E-09 |
| GO:0006546 | glycine catabolic process | 11 | 9 | 1.92 | 5.8E-06 |
| GO:0005975 | carbohydrate metabolic process | 1345 | 320 | 234.82 | 0.000013 |
| GO:0006073 | cellular glucan metabolic process | 142 | 56 | 24.79 | 0.000026 |
| GO:0006260 | DNA replication | 119 | 55 | 20.78 | 0.000027 |
| GO:0000910 | cytokinesis | 24 | 12 | 4.19 | 0.000033 |
| GO:0006629 | lipid metabolic process | 928 | 234 | 162.02 | 0.00028 |
| GO:0030244 | cellulose biosynthetic process | 62 | 22 | 10.82 | 0.00051 |
| GO:0000096 | sulfur amino acid metabolic process | 50 | 18 | 8.73 | 0.00084 |
| GO:0006656 | phosphatidylcholine biosynthetic process | 4 | 4 | 0.7 | 0.00093 |
| GO:0018160 | peptidyl-pyrromethane cofactor linkage | 4 | 4 | 0.7 | 0.00093 |
| GO:1901070 | guanosine-containing compound biosynthetic process | 17 | 9 | 2.97 | 0.00094 |
| GO:0006418 | tRNA aminoacylation for protein translation | 95 | 29 | 16.59 | 0.00125 |
| GO:0009132 | nucleoside diphosphate metabolic process | 135 | 40 | 23.57 | 0.00155 |
| GO:0006228 | UTP biosynthetic process | 15 | 8 | 2.62 | 0.00171 |
| GO:0006241 | CTP biosynthetic process | 15 | 8 | 2.62 | 0.00171 |
| GO:0006269 | DNA replication, synthesis of RNA primer | 5 | 4 | 0.87 | 0.00399 |
| GO:0045132 | meiotic chromosome segregation | 5 | 4 | 0.87 | 0.00399 |
| GO:0009084 | glutamine family amino acid biosynthetic process | 31 | 12 | 5.41 | 0.00416 |
| GO:1901617 | organic hydroxy compound biosynthetic process | 23 | 14 | 4.02 | 0.00531 |
| GO:0009234 | menaquinone biosynthetic process | 3 | 3 | 0.52 | 0.00532 |
| GO:0016117 | carotenoid biosynthetic process | 14 | 7 | 2.44 | 0.00536 |
| GO:0009065 | glutamine family amino acid catabolic process | 12 | 6 | 2.1 | 0.00997 |
| GO:0046168 | glycerol-3-phosphate catabolic process | 6 | 4 | 1.05 | 0.01031 |
| GO:0015671 | oxygen transport | 6 | 4 | 1.05 | 0.01031 |
| GO:0006801 | superoxide metabolic process | 23 | 9 | 4.02 | 0.01161 |
| GO:0007076 | mitotic chromosome condensation | 13 | 6 | 2.27 | 0.01582 |
| GO:0006166 | purine ribonucleoside salvage | 4 | 3 | 0.7 | 0.01849 |
| GO:0006096 | glycolytic process | 114 | 29 | 19.9 | 0.02014 |
| GO:0046274 | lignin catabolic process | 33 | 11 | 5.76 | 0.02045 |
| GO:0042549 | photosystem II stabilization | 7 | 4 | 1.22 | 0.02075 |
| GO:0042026 | protein refolding | 14 | 6 | 2.44 | 0.02366 |
| GO:0019307 | mannose biosynthetic process | 2 | 2 | 0.35 | 0.03047 |
| GO:0007155 | cell adhesion | 2 | 2 | 0.35 | 0.03047 |
| GO:0045038 | protein import into chloroplast thylakoid membrane | 2 | 2 | 0.35 | 0.03047 |
| GO:0048478 | replication fork protection | 2 | 2 | 0.35 | 0.03047 |
| GO:0007623 | circadian rhythm | 2 | 2 | 0.35 | 0.03047 |
| GO:0010027 | thylakoid membrane organization | 2 | 2 | 0.35 | 0.03047 |
| GO:0006450 | regulation of translational fidelity | 2 | 2 | 0.35 | 0.03047 |
| GO:0030259 | lipid glycosylation | 15 | 6 | 2.62 | 0.03373 |
| GO:0009082 | branched-chain amino acid biosynthetic process | 23 | 8 | 4.02 | 0.03537 |
| GO:0006168 | adenine salvage | 5 | 3 | 0.87 | 0.04023 |
| GO:0010207 | photosystem II assembly | 5 | 3 | 0.87 | 0.04023 |
| GO:0006353 | DNA-templated transcription, termination | 5 | 3 | 0.87 | 0.04023 |
| GO:0006662 | glycerol ether metabolic process | 68 | 18 | 11.87 | 0.04094 |
| Overrepresented in the subset of up-regulated in systemic infection | |||||
| GO:0006032 | chitin catabolic process | 31 | 7 | 0.78 | 9.1E-06 |
| GO:0006355 | regulation of transcription, DNA-templated | 1764 | 69 | 44.11 | 0.00012 |
| GO:0005975 | carbohydrate metabolic process | 1345 | 63 | 33.64 | 0.00022 |
| GO:0043562 | cellular response to nitrogen levels | 2 | 2 | 0.05 | 0.00062 |
| GO:0009744 | response to sucrose | 2 | 2 | 0.05 | 0.00062 |
| GO:0016998 | cell wall macromolecule catabolic process | 29 | 5 | 0.73 | 0.00069 |
| GO:0019310 | inositol catabolic process | 8 | 3 | 0.2 | 0.00079 |
| GO:0005992 | trehalose biosynthetic process | 34 | 5 | 0.85 | 0.00146 |
| GO:0015770 | sucrose transport | 3 | 2 | 0.08 | 0.00184 |
| GO:0019953 | sexual reproduction | 11 | 3 | 0.28 | 0.00221 |
| GO:0009607 | response to biotic stimulus | 43 | 6 | 1.08 | 0.00271 |
| GO:0006570 | tyrosine metabolic process | 5 | 2 | 0.13 | 0.00594 |
| GO:0006094 | gluconeogenesis | 8 | 2 | 0.2 | 0.01581 |
| GO:0006952 | defense response | 112 | 8 | 2.8 | 0.01862 |
| GO:0006541 | glutamine metabolic process | 23 | 3 | 0.58 | 0.01898 |
| GO:0000272 | polysaccharide catabolic process | 25 | 3 | 0.63 | 0.02376 |
| GO:0006662 | glycerol ether metabolic process | 68 | 5 | 1.7 | 0.02756 |
| GO:0003333 | amino acid transmembrane transport | 46 | 4 | 1.15 | 0.02758 |
| GO:0006529 | asparagine biosynthetic process | 11 | 2 | 0.28 | 0.02956 |
| GO:0008283 | cell proliferation | 11 | 2 | 0.28 | 0.02956 |
| GO:0044264 | cellular polysaccharide metabolic process | 148 | 7 | 3.7 | 0.03961 |
| GO:0008272 | sulfate transport | 31 | 3 | 0.78 | 0.04163 |
| GO:0006857 | oligopeptide transport | 33 | 3 | 0.83 | 0.04874 |
| Overrepresented in the subset of down-regulated in systemic infection | |||||
| GO:0007018 | microtubule-based movement | 129 | 11 | 0.7 | 1.2E-10 |
| GO:0000079 | regulation of cyclin-dependent protein serine/threonine kinase activity | 48 | 7 | 0.26 | 7.2E-09 |
| GO:0007067 | mitotic nuclear division | 51 | 5 | 0.28 | 0.0001 |
| GO:0016114 | terpenoid biosynthetic process | 30 | 2 | 0.16 | 0.0116 |
| GO:0006265 | DNA topological change | 30 | 2 | 0.16 | 0.0116 |
| GO:0007094 | mitotic spindle assembly checkpoint | 3 | 1 | 0.02 | 0.0163 |
| GO:0006952 | defense response | 112 | 3 | 0.61 | 0.0235 |
| GO:0009813 | flavonoid biosynthetic process | 6 | 1 | 0.03 | 0.0323 |
| GO:0030244 | cellulose biosynthetic process | 62 | 2 | 0.34 | 0.0452 |
| Overrepresented in the subset of up-regulated genes common to local and systemic infections | |||||
| GO:0043562 | cellular response to nitrogen levels | 2 | 2 | 0.01 | 0.000041 |
| GO:0009744 | response to sucrose | 2 | 2 | 0.01 | 0.000041 |
| GO:0005992 | trehalose biosynthetic process | 34 | 4 | 0.22 | 0.000066 |
| GO:0006094 | gluconeogenesis | 8 | 2 | 0.05 | 0.0011 |
| GO:0019310 | inositol catabolic process | 8 | 2 | 0.05 | 0.0011 |
| GO:0006529 | asparagine biosynthetic process | 11 | 2 | 0.07 | 0.0022 |
| GO:0006355 | regulation of transcription, DNA-templated | 1764 | 21 | 11.37 | 0.0043 |
| GO:0007205 | protein kinase C-activating G-protein coupled receptor signaling pathway | 24 | 2 | 0.15 | 0.0104 |
| GO:0006659 | phosphatidylserine biosynthetic process | 3 | 1 | 0.02 | 0.0192 |
| GO:0042742 | defense response to bacterium | 4 | 1 | 0.03 | 0.0255 |
| GO:0006562 | proline catabolic process | 4 | 1 | 0.03 | 0.0255 |
| GO:0050832 | defense response to fungus | 4 | 1 | 0.03 | 0.0255 |
| GO:0006570 | tyrosine metabolic process | 5 | 1 | 0.03 | 0.0318 |
| GO:0003333 | amino acid transmembrane transport | 46 | 2 | 0.3 | 0.0355 |
| GO:0009064 | glutamine family amino acid metabolic process | 57 | 3 | 0.37 | 0.0453 |
| Overrepresented in the subset of down-regulated genes common to local and systemic infections | |||||
| GO:0007018 | microtubule-based movement | 129 | 10 | 0.43 | 1.4E-11 |
| GO:0000079 | regulation of cyclin-dependent protein serine/threonine kinase activity | 48 | 7 | 0.16 | 2.1E-10 |
| GO:0007067 | mitotic nuclear division | 51 | 5 | 0.17 | 0.000014 |
| GO:0006265 | DNA topological change | 30 | 2 | 0.1 | 0.0045 |
| GO:0007094 | mitotic spindle assembly checkpoint | 3 | 1 | 0.01 | 0.0099 |
| GO:0030244 | cellulose biosynthetic process | 62 | 2 | 0.21 | 0.0181 |
| GO:0006606 | protein import into nucleus | 12 | 1 | 0.04 | 0.0392 |